Snakemake Report

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Workflow

Click the nodes to obtain details about each step.

QC

Trim Stats

Statistics

If the workflow has been executed in cluster/cloud, runtimes include the waiting time in the queue.

Configuration

File Code

out_dir:
    '/Users/csifuentes/Documents/rnaseq-demo'
input_dir:
    fastq: '/Users/csifuentes/Documents/fastq-input/rnaseq_raw_data'
    genome_fasta: '/Users/csifuentes/Documents/fastq-input/rnaseq_raw_data/indexes/Homo_sapiens.GRCh38.dna.chromosome.19.fa'
    genome_gtf: '/Users/csifuentes/Documents/fastq-input/rnaseq_raw_data/indexes/hg38chr19.gtf'
thread_info:
    alignment: 8
    fastqc: 2
    index: 8
    trim: 8
    deeptools: 8
    pepr: 8
    homer: 8
trim:
    trimq: 20
    minlen: 30

Jobs 4

Input files

/Users/csifuentes/Documents/fastq-input/rnaseq_raw_data/{sample}.fastq.gz

Output files

/Users/csifuentes/Documents/rnaseq-demo/QC/{sample}_fastqc.zip

Conda software stack

fastqc=0.11.9
font-ttf-dejavu-sans-mono=2.37
fontconfig=2.13.1
freetype=2.10.4
icu=58.2
libcxx=10.0.0
libiconv=1.16
libpng=1.6.37
libxml2=2.9.10
openjdk=11.0.6
perl=5.26.2
xz=5.2.5
zlib=1.2.11

Code

1
2
3

        mkdir -p {params.qc_dir}
        fastqc         --noextract         -f {params.format}         -o {params.qc_dir}         -t {threads}         {input.fastq}

Jobs 2

Input files

/Users/csifuentes/Documents/fastq-input/rnaseq_raw_data/{sample}_1.fastq.gz
/Users/csifuentes/Documents/fastq-input/rnaseq_raw_data/{sample}_2.fastq.gz

Output files

/Users/csifuentes/Documents/rnaseq-demo/TRIM/{sample}_1.trimmed.fastq.gz
/Users/csifuentes/Documents/rnaseq-demo/TRIM/{sample}_2.trimmed.fastq.gz
/Users/csifuentes/Documents/rnaseq-demo/TRIM/{sample}.html
/Users/csifuentes/Documents/rnaseq-demo/TRIM/{sample}.json

Conda software stack

fastp=0.20.1
libcxx=10.0.0
zlib=1.2.11

Code

1 2	`fastp -i {input.r1} -I {input.r2} -o {output.r1} -O {output.r2} -w {threads} -h {output.html} -j {output.json} -G -l {params.minlen} -q {params.trimq}`